Project name: Hunter_Project_023
Run name: 191217_NB551164_0202_AHWNJWAFXY
Read type: Paired-end 76bp
Samples: 18
Total read-pairs: 185,929,565
Mean read-pairs per sample: 10,329,420
Report generated: Thu Dec 19 17:17:07 CST 2019

Instrument: nextseq NextSeq Mid

More details
Fastq folder: /panfs/roc/umgc/illumina_analysis/191217_NB551164_0202_AHWNJWAFXY-analysis/demultiplex_20191219-17-12-49/demultiplex/Hunter_Project_023
Commandline: /panfs/roc/groups/3/umii/public/gopher-pipelines/2.0/bin/illumina-pipeline.pl –fastqfolder /panfs/roc/umgc/illumina_analysis/191217_NB551164_0202_AHWNJWAFXY-analysis/demultiplex_20191219-17-12-49/demultiplex/Hunter_Project_023 –samplespernode 20 –threadspersample 6 –projectname Hunter_Project_023 –runname 191217_NB551164_0202_AHWNJWAFXY –illuminasamplesheet /panfs/roc/umgc/illumina_analysis/191217_NB551164_0202_AHWNJWAFXY-analysis/demultiplex_20191219-17-12-49/SampleSheet.csv –threads 20 –scratchfolder /panfs/roc/umgc/tmp/scratch/191217_NB551164_0202_AHWNJWAFXY/demultiplex_20191219-17-12-49/Hunter_Project_023/illumina-basicQC
Gopher-pipelines version: 2.0
Program versions
R/3.5.0
advisor/2018/release
bowtie2/2.3.4.1
bzip2/1.0.6-gnu6.1.0_PIC
bzip2/1.0.6-gnu7.2.0_PIC
curl/7.59.0_gcc7.2.0
ensembl/1.0
fastqc/0.11.7
gcc/7.2.0
gcc/8.1.0
genomes-other/1.0
genomes/1.0
gmp/6.1.2_gcc7.2.0
gmp/6.1.2_gcc8.1.0
gopher-pipelines/2.0
gtools/2.0
impi/2018/release_singlethread
inspector/2018/release
intel/2018/release
intel/cluster/2018
isl/0.18_gcc7.2.0
isl/0.19_gcc8.1.0
itac/2018/release
jdk1.7.0_45
libtiff/4.0.8
mpc/1.0.3_gcc7.2.0
mpc/1.1.0_gcc8.1.0
mpfr/3.1.6_gcc7.2.0
mpfr/4.0.1_gcc8.1.0
pandoc/2.3
parallel/20180922
pcre/8.42_gcc7.2.0
plotly/20190228
pysam/0.15.3
python2/2.7.12_anaconda4.2
python3/3.6.3_anaconda5.0.1
samtools/1.9
texlive/20131202
trimmomatic/0.33
umgc/1.0
vtune/2018/release
xz-utils/5.2.3_gcc7.2.0
zlib/1.2.11_gcc7.2.0
zlib/1.2.8
Metric table
general.projectname general.readlength general.readlengthr2 general.runname subsample.rawreads subsample.subsampledreads fastqc.meanreadqualityR1 fastqc.meanreadqualityR2 fastqc.pct.adapter fastqc.pct.deduplicated fastqc.pct.dimer fastqc.pct.gc fastqc.sequencelength fastqc.totalsequences fastqspeciesscreen.pct.Adapters fastqspeciesscreen.pct.Chloroplast fastqspeciesscreen.pct.Mitochondria fastqspeciesscreen.pct.NoHit fastqspeciesscreen.pct.PhiX fastqspeciesscreen.pct.Vectors fastqspeciesscreen.pct.ecoli fastqspeciesscreen.pct.human fastqspeciesscreen.pct.mouse fastqspeciesscreen.pct.rRNA
234.1 Hunter_Project_023 76 76 191217_NB551164_0202_AHWNJWAFXY 7082713 7082713 33.60 32.70 0 31.50 0 39.00 76 2e+06 0 0.03 0 98.75 0 0.88 0.24 0.06 0.00 0.04
234.2 Hunter_Project_023 76 76 191217_NB551164_0202_AHWNJWAFXY 9509522 9509522 33.70 33.50 0 33.12 0 34.00 76 2e+06 0 0.07 0 99.23 0 0.63 0.00 0.00 0.00 0.07
234.3 Hunter_Project_023 76 76 191217_NB551164_0202_AHWNJWAFXY 10125530 10125530 33.70 33.50 0 33.30 0 34.00 76 2e+06 0 0.05 0 99.27 0 0.65 0.00 0.00 0.00 0.03
243.1 Hunter_Project_023 76 76 191217_NB551164_0202_AHWNJWAFXY 11358507 11358507 33.80 33.60 0 34.28 0 35.00 76 2e+06 0 0.01 0 98.82 0 1.05 0.04 0.00 0.00 0.08
243.2 Hunter_Project_023 76 76 191217_NB551164_0202_AHWNJWAFXY 11148778 11148778 33.70 32.70 0 36.15 0 35.00 76 2e+06 0 0.04 0 99.01 0 0.93 0.00 0.00 0.00 0.02
243.3 Hunter_Project_023 76 76 191217_NB551164_0202_AHWNJWAFXY 10376560 10376560 33.70 33.50 0 34.88 0 34.00 76 2e+06 0 0.02 0 98.80 0 1.14 0.00 0.01 0.00 0.03
262.1 Hunter_Project_023 76 76 191217_NB551164_0202_AHWNJWAFXY 11789038 11789038 33.70 33.50 0 31.94 0 35.00 76 2e+06 0 0.05 0 98.22 0 1.33 0.35 0.00 0.02 0.03
262.2 Hunter_Project_023 76 76 191217_NB551164_0202_AHWNJWAFXY 10551493 10551493 33.70 33.50 0 31.22 0 35.00 76 2e+06 0 0.03 0 98.65 0 1.25 0.02 0.00 0.00 0.05
262.3 Hunter_Project_023 76 76 191217_NB551164_0202_AHWNJWAFXY 9354962 9354962 33.50 31.90 0 33.35 0 35.00 76 2e+06 0 0.01 0 99.20 0 0.73 0.01 0.00 0.01 0.04
MMM.1.OCT2019 Hunter_Project_023 76 76 191217_NB551164_0202_AHWNJWAFXY 11079312 11079312 33.70 33.60 0 32.41 0 35.00 76 2e+06 0 0.01 0 98.51 0 1.40 0.01 0.03 0.00 0.04
MMM.2.OCT2019 Hunter_Project_023 76 76 191217_NB551164_0202_AHWNJWAFXY 10585133 10585133 33.70 33.50 0 32.32 0 35.00 76 2e+06 0 0.08 0 98.64 0 1.24 0.00 0.00 0.00 0.04
MMM.3.OCT2019 Hunter_Project_023 76 76 191217_NB551164_0202_AHWNJWAFXY 10368310 10368310 33.70 33.50 0 32.81 0 35.00 76 2e+06 0 0.05 0 98.08 0 1.82 0.00 0.01 0.00 0.04
MMM.GLU.1.OCT2019 Hunter_Project_023 76 76 191217_NB551164_0202_AHWNJWAFXY 10390552 10390552 33.70 32.60 0 34.59 0 35.00 76 2e+06 0 0.04 0 99.25 0 0.66 0.02 0.01 0.00 0.02
MMM.GLU.2.OCT2019 Hunter_Project_023 76 76 191217_NB551164_0202_AHWNJWAFXY 9314880 9314880 33.70 33.30 0 33.86 0 35.00 76 2e+06 0 0.04 0 99.24 0 0.68 0.01 0.00 0.00 0.03
MMM.GLU.3.OCT2019 Hunter_Project_023 76 76 191217_NB551164_0202_AHWNJWAFXY 10368946 10368946 33.80 33.60 0 32.87 0 34.00 76 2e+06 0 0.04 0 99.12 0 0.72 0.01 0.07 0.02 0.02
MMM.LACCAA.1.OCT2019 Hunter_Project_023 76 76 191217_NB551164_0202_AHWNJWAFXY 10099424 10099424 33.70 33.00 0 32.95 0 35.00 76 2e+06 0 0.05 0 98.51 0 1.37 0.00 0.01 0.01 0.05
MMM.LACCAA.2.OCT2019 Hunter_Project_023 76 76 191217_NB551164_0202_AHWNJWAFXY 11016966 11016966 33.80 33.50 0 31.94 0 35.00 76 2e+06 0 0.05 0 98.57 0 1.27 0.03 0.02 0.00 0.06
MMM.LACCAA.3.OCT2019 Hunter_Project_023 76 76 191217_NB551164_0202_AHWNJWAFXY 11408939 11408939 33.80 33.60 0 31.52 0 34.00 76 2e+06 0 0.06 0 98.70 0 1.14 0.01 0.00 0.03 0.06
Mean undef 76 76 191217_NB551164_0202_AHWNJWAFXY 10329420 10329420 33.71 33.26 0 33.06 0 34.94 76 2e+06 0 0.04 0 98.81 0 1.05 0.04 0.01 0.01 0.04

Order samples by

Read-pairs per Sample

The number of read-pairs per sample at the start of the analysis is shown.

Quality Summary (R1)

This plot shows the mean base quality score for each position in a fastq file. The higher the score the better the base call. Green indicates very good quality, yellow indicates reasonable quality, and red indicates poor quality. The quality of calls degrade as the sequencing run progresses, so it is common to see base calls turning yellow towards the end of a read. It is common to see base calls turning red in short insert libraries (16s/18s, small RNA, amplicon). R2 read quality is typically slightly lower overall than R1 read quality. This metric is calculated by FastQC.

Quality Summary (R2)

This plot shows the mean base quality score for each position in a fastq file. The higher the score the better the base call. Green indicates very good quality, yellow indicates reasonable quality, and red indicates poor quality. The quality of calls degrade as the sequencing run progresses, so it is common to see base calls turning yellow towards the end of a read. It is common to see base calls turning red in short insert libraries (16s/18s, small RNA, amplicon). R2 read quality is typically slightly lower overall than R1 read quality. This metric is calculated by FastQC.

Adapter Content

This plot shows the cumulative proportion of each sample in which sequencing adapter sequences have been seen at each position. Once an adapter sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages only increase as the read length goes on. It is common to see significant adapter sequence content at the ends of reads in short insert libraries (16s/18s, small RNA, amplicon). This metric is calculated by FastQC.

Library Diversity

This plot shows the percentage of R1 reads that remain after deduplication (removing duplicated sequences), which is a measure of library diversity. Sequence data from genomic DNA libraries typically have high library diversity, and data from targeted sequencing libraries typically have low diversity. This metric is calculated by FastQC.

Sequence Content

The first 10,000 R1 reads from each sample are aligned to a selection of common reference genomes and sequence contaminants, and the number of reads aligning to each reference is shown. Reads aligning to multiple references are assigned to the reference with the most alignments. This plot provides a simple method to verify the sequence content of each library.